The aim of this study is to establish a certain Quantitative Structure-Activity Relationship (QSAR) between compound molecular characteristics and nanofiltration (NF) separation efficiency. Measurements were carried out in a crossflow NF unit and using ten organic compounds (ethanol, butyl alcohol, glycerin, phenol, glucose, sorbitolum, dodecanoic acid, Imidacloprid, sucrose and Dimethomorph) in aqueous solution and two commercial NF membranes (DK and NF90). Four kind compound characteristics of Molecular weight (Mw), Octanol-Water Partition Coefficient (logP), Molar Refraction (CMR), Henry’s law (H) are selected. Through regression, F test and t test, QSAR analysis was accomplished to prove the validity of regression equation with confidence probability of equation coefficient above 85%. It could be concluded that Mw contributed most to rejection of DK and NF90 according to QSAR at constant flux (500mg/L) and feed concentration (500mg/L). The contribution of CMR is less than MW for NF90 rejection, following by logP, H.